metaspace_converter.anndata_to_array module

metaspace_converter.anndata_to_array.anndata_to_image_array(adata, layer=None)[source]

Extracts an array of ion images from an AnnData object (that has been generated through the metaspace_to_anndata function).

Parameters:

  • adata (AnnData) – An AnnData object.

  • layer (Optional[str]) – AnnData.layer that should be extracted to an image array. Default is None, which means that adata.X will be used.

Return type:

ndarray

Returns:

A three-dimensional Numpy array in the following shape

  • Dimension 0: Number of ion images in the order of adata.var_names

  • Dimension 1: Image height adata.uns["metaspace"]["image_size"]["y"]

  • Dimension 2: Image width adata.uns["metaspace"]["image_size"]["x"]

Raises:

ValueError – If the AnnData object has been modified. E.g. Pixel have been removed/added and the number of pixels and their coordinates do not match the original image dimensions.